In the intestine, a number of anti-inflammatory, regulatory, and defense mechanisms maintain the integrity of the epithelial barrier and limit intestinal damage. These mechanisms are altered in diseases such as Crohn's disease (CD) and celiac disease (CeD). Shared features of these disorders include increased proinflammatory cytokine production by immune cells, expansion of effector T cells, and breakdown of the epithelial barrier. While environmental, dietary, and genetic factors are linked to these diseases, the precise mechanisms leading to immune dysregulation are unknown. Relevant to this proposal, biopsies taken from the inflamed tissues of CeD and CD patients reveal increased activity of the pro-inflammatory NF- ?B pathway; however how this occurs is not understood. Recent analysis of genome wide association studies indicates that a number of inflammatory diseases share common single nucleotide polymorphisms (SNPs). Interestingly, the majority of these SNPs reside in noncoding regions, but how this contributes to disease development has not been fully addressed. Recent analyses of long noncoding RNAs (LncRNAs) have demonstrated that they play key roles in regulating gene expression at the level of epigenetic modification, translation, and transcription. However, the lncRNA field is stil in its infancy, and the majority of lncRNAs are uncharacterized, especially from an immunological perspective. An overall goal of this proposal is to determine how changes in lncRNAs contribute to the dysregulated inflammation during CeD and CD. To this end, in preliminary studies, the Ghosh lab has identified loci of putative human lncRNAs that contain CeD- and CD-associated SNPs, and are conserved with novel mouse lncRNAs. Our data identifies mouse lnc15 as a disease-associated, conserved lncRNA, and that lnc15 expression is decreased in response to LPS-induced NF- ?B activation, and inversely correlated to IL-6, IL-12 and TNF-a expression. The first aim of this study proposes to characterize and annotate human lnc15 using molecular approaches and will determine inflammatory genes significantly correlated with lnc15 expression. Targeting approaches will determine the effects of overexpression or silencing of lnc15 on the expression of these pro-inflammatory NF- ?B targets. Next we will ask whether changes in lnc15 are associated with CeD or CD by analyzing its expression in patient biopsy samples. To determine the mechanisms by which lnc15 functions, we will identify RNA binding partners (protein, RNA, DNA) by chromatin isolation by RNA purification. Moreover, we will determine if SNPs in lncRNAs change the binding partners/binding affinity. These data could identify a mechanistic basis for how SNPs in non-coding regions contribute to the complex disease traits associated with CeD/CD. Finally, to determine if deletion of lnc15 results in changes in intestinal inflammation we will use the CRISPR/Cas9 strategy to generate mouse models directly relevant to study CD and CeD. We anticipate that these proposed studies will lead to a better understanding of the mechanisms by which genetic factors predispose patients to intestinal disease and will have important therapeutic implications.